SOAPdenovo-Trans specifications

Information

Unique identifier	OMICS_01324
Name	SOAPdenovo-Trans
Software type	Package/Module
Interface	Command line interface
Restrictions to use	None
Operating system	Unix/Linux
Programming languages	C, C++
License	GNU General Public License version 3.0
Computer skills	Advanced
Version	1.0.4
Stability	Stable
Maintained	Yes

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Documentation

Maintainer

Yinlong Xie <>

Publication for SOAPdenovo-Trans

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

2014 Bioinformatics

PMID: 24532719

SOAPdenovo-Trans IN pipelines

(2)

Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei

2015

PMCID: 4521149

PMID: 26228545

DOI: 10.1038/srep12525

[…] shows 98% nucleic acid identity to genbank accession af037324 over its entire length. however, very few rna-seq reads align to this locus and the transcript is not fully reconstructed using soapdenovo-trans or cufflinks. the translation of the predicted gene aligns with the protein sequence of the t. castaneum gaba receptor isoform x1 (blast e-value 0.0, 77% amino acid identity) […]

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome

2015

PMCID: 4652390

PMID: 26582032

DOI: 10.1186/s12864-015-2111-2

[…] high-confidence mapping fragments. library-specific insert sizes were estimated by mapping the trimmed reads to the pig transcriptome. the unmapped read pairs were assembled into transcripts using soapdenovo-trans-31kmer (version 1.02) and aligned to the ncbi nucleotide database (version as of 2012-09-12)., fantom5 human and mouse samples: please refer to the methods section […]

SOAPdenovo-Trans institution(s)

School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China; BGI-Shenzhen, Shenzhen, China; HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong; Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha, China; BGI-tech, BGI-Shenzhen, Shenzhen, China; Department of Medicine, University of Alberta, Edmonton, Canada; Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Department of Biological Sciences, University of Alberta, Edmonton, Canada; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Department of Biology, University of Copenhagen, Copenhagen, Denmark;Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia

SOAPdenovo-Trans funding source(s)

Supported by The State Key Development Program for Basic Research of China-973 Program (NO.2011CB809202), Shenzhen Key Laboratory of Transomics Biotechnologies (CXB201108250096A), China National GeneBank and the 1000 plants (1KP) initiative.

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